JAL-2962 code tidying/documentation (non-functional) changes

[jalview.git] / src / jalview / datamodel / SequencePoint.java

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index a8b0503..28db278 100755 (executable)
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,51 +1,55 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A bean that models a point with (x, y, z) coordinates and a reference to a
+ * sequence
  */
 public class SequencePoint
 {
-  // SMJS PUBLIC
-  /**
-   * for points with no real physical association with an alignment sequence
+  /*
+   * Associated alignment sequence, or dummy sequence object
    */
-  public boolean isPlaceholder = false;
+  private final SequenceI sequence;
 
-  /**
-   * Associated alignment sequence, or dummy sequence object.
+  /*
+   * array of coordinates in embedded sequence space
    */
-  public SequenceI sequence;
+  public float[] coord;
 
   /**
-   * array of coordinates in embedded sequence space.
+   * Constructor
+   * 
+   * @param sequence
+   * @param coord
    */
-  public float[] coord;
-
-  // SMJS ENDPUBLIC
   public SequencePoint(SequenceI sequence, float[] coord)
   {
     this.sequence = sequence;
     this.coord = coord;
   }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
 }